Christopher T. Lee, Ph.D.

Hartwell Foundation Postdoctoral Fellow, Rangamani and Holst Labs

Publications

You can also find my articles on my more frequently updated Google Scholar profile.
Key: Icons link to DOI , biorxiv , arxiv ;
    * denotes equal contribution; $ denotes corresponding author

Submitted and In Preparation

  • Mem3DG: An open-source software framework for 3-Dmembrane mechanochemical dynamics using discretedifferential geometry on triangulated meshes

    C. Zhu, C. T. Lee, R. Ramamoorthi, and P. Rangamani$
    Status: In Preparation     More info →

  • Stochastic Simulations Reveal That Dendritic Spine Morphology Regulates Synaptic Plasticity in a Deterministic Manner

    M. V. Holst*, M. K. Bell*, C. T. Lee, and P. Rangamani$
    Status: In Review     Preprint: bioRxiv More info →

  • Independent Markov Decomposition: Towards Modeling Kinetics of Biomolecular Complexes

    T. Hempel, M. J. Razo*, C. T. Lee*, B. C. Taylor*, R. E. Amaro$, and F. Noé$
    Status: Submitted     Preprint: bioRxiv More info →

  • Morphological Principles of Neuronal Mitochondria

    R. Mendelsohn*, G. C. Garcia*, T. M. Bartol, C. T. Lee, P. Khandelwal, E. Liu, D. J. Spencer, A. Husar, E. A. Bushong, S. Phan, G. Perkins, M. H. Ellisman, A. Skupin, T. J. Sejnowski$, and P. Rangamani$
    Status: In Review     Preprint: bioRxiv More info →

  • Benchmarking ensemble docking methods in D3R Grand Challenge 4

    J. L. Gan, D. Kumar, C. Chen, B. C. Taylor, B. R. Jagger, R. E. Amaro$, and C. T. Lee$
    Status: In Review     Preprint: bioRxiv More info →

Peer Reviewed and In Press

Sorted by year

  1. Value of Models for Membrane Budding

    Curr. Opin. Cell Biol. (2021) DOI
    C. T. Lee, M. Akamatsu, and P. Rangamani$ More info →

  2. Independent Markov Decomposition: Towards modeling kinetics of biomolecular complexes

    Proc. Natl. Acad. Sci. (2021) DOI bioRxiv
    T. Hempel, M. J. Razo*, C. T. Lee*, B. C. Taylor*, R. E. Amaro$, and F. Noé$ More info →

  3. Applications and Challenges of Machine Learning to Enable Realistic Cellular Simulations

    Front. Phys. (2021) DOI arXiv
    R. Vasan, M. P. Rowan, C. T. Lee, G. R. Johnson, P. Rangamani, and M. Holst$ More info →

  4. 3D Mesh Processing Using GAMer 2 to Enable Reaction-Diffusion Simulations in Realistic Cellular Geometries

    PLOS Comp. Biol. (2020) DOI arXiv bioRxiv
    C. T. Lee*, J. G. Laughlin*, N. La Beaumelle, R. E. Amaro, J. A. McCammon, R. Ramamoorthi, M. J. Holst, and P. Rangamani$ More info →

  5. An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries

    Biophys. J. (2020) DOI arXiv bioRxiv
    C. T. Lee$, J. G. Laughlin, J. B. Moody, R. E. Amaro, J. A. McCammon, M. J. Holst, and P. Rangamani$ More info →

  6. The Implementation of the Colored Abstract Simplicial Complex and Its Application to Mesh Generation

    ACM Trans. Math. Softw. (2019) DOI arXiv
    C. T. Lee*$, J. B. Moody*, R. E. Amaro, J. A. Mccammon, and M. J. Holst More info →

  7. Structural Basis for Ligand Modulation of the CCR2 Conformational Landscape

    Proc. Natl. Acad. Sci. (2019) DOI bioRxiv
    B. C. Taylor, C. T. Lee, and R. E. Amaro$ More info →

  8. Quantitative Ranking of β-cyclodextrin Ligand Binding Kinetics With SEEKR, a Hybrid MD/BD/Milestoning Approach

    J. Phys. Chem. Lett. (2018) DOI ChemRxiv: ChemRxiv
    B. R. Jagger, C. T. Lee, and R. E. Amaro$ More info →

  9. Exascale Computing: A New Dawn for Computational Biology

    Comput. Sci. Eng. (2018) DOI
    C. T. Lee, and R. E. Amaro$ More info →

  10. Two Relations to Estimate Membrane Permeability Using Milestoning

    J. Phys. Chem. B (2016) DOI
    L. W. Votapka*, C. T. Lee*, and R. E. Amaro$ More info →

  11. Emerging Computational Methods for the Rational Discovery of Allosteric Drugs

    Chem. Rev. (2016) DOI
    J. R. Wagner*, C. T. Lee*, J. D. Durrant, R. D. Malmstrom, V. A. Feher, and R. E. Amaro$ More info →

  12. Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds

    J. Chem. Inf. Model. (2016) DOI
    C. T. Lee, J. Comer$, C. Herndon, N. Leung, A. Pavlova, R. V. Swift, C. Tung, C. N. Rowley, R. E. Amaro$, C. Chipot$, Y. Wang$, and J. C. Gumbart$ More info →

  13. Known Structure, Unknown Function: An Inquiry-Based Undergraduate Biochemistry Laboratory Course

    Biochem. Mol. Biol. Educ. (2015) DOI
    C. Gray*, C. W. Price*, C. T. Lee, A. H. Dewald, M. A. Cline, C. E. McAnany, L. Columbus$, and C. Mura$ More info →

  14. Application of Molecular-Dynamics Based Markov State Models to Functional Proteins

    J. Chem. Theory Comput. (2014) DOI
    R. D. Malmstrom, C. T. Lee, A. T. Van Wart, and R. E. Amaro$ More info →